Need help ASAP

We've just had my car jacked up, and changed the haldex controller to see if it would cure my intermittent 2wd/4wd fault. We've let the car back down, went to start it, and it won't even turn over. And it's flashing up on the screen with a brake problem. But It won't even connect to vagcom now. We've tried taking the battery off for a bit, and it still wouldn't do anything after that. Any next ideas?

We did think that could have been a possibility, but it's been jacked up plenty times before without issue.
That would only effect the alarm/immobiliser though. This is showing a brake fault (although it won't tell you what) and it won't let vagcom connect to the car for some reason.

My mate thinks that the ecu isn't getting a live signal when the ignition is turned on. He says it needs a couple of lives to work. A battery live, an ignition live and maybes another.
The fact that it's not letting vagcom connect, is the reason he thinks one of the live signals must have been affected. We've checked all fuses and relays and they're all fine.
The only other thing he thinks it could be is an anti-tow thing on the alarm (a Clifford) because we've had it jacked up quite high. Only thing is, if it is the alarm that's taken away a live signal, as a security measure, we don't know how to disable it.